Contacts of the strand formed by residues 326 - 332 (chain G) in PDB entry 3QS7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 326 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287G LEU* 4.2 9.4 - - - -
288G GLU* 5.7 3.4 - - - -
324G ASP 3.6 2.2 + - - -
325G THR* 1.3 73.7 - - - +
327G TYR* 1.4 59.5 + - - -
328G TYR* 3.2 16.1 - - - -
341G LEU* 4.5 1.8 - - - -
342G VAL* 2.9 33.7 + - - +
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Residues in contact with TYR 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G LEU* 3.0 31.1 - - - +
288G GLU* 3.9 10.7 - - + +
326G GLY* 1.4 68.3 - - - -
328G TYR* 1.3 60.3 + - - +
329G THR* 5.2 0.9 - - - +
339G SER* 6.0 3.4 - - - -
340G ALA 3.9 5.6 - - - +
341G LEU* 4.0 14.8 - - + +
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Residues in contact with TYR 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268G LEU* 4.0 18.8 - - + +
270G ILE* 4.8 15.9 - - + -
285G TRP* 4.2 17.2 - + + -
286G GLU 3.3 5.2 - - - -
287G LEU* 3.5 36.8 - - + +
292G LEU* 3.8 23.8 - - + -
315G ALA* 5.7 0.9 - - + -
317G VAL* 4.6 5.1 - - + +
324G ASP* 2.7 36.2 + - - +
326G GLY 3.2 25.1 - - - -
327G TYR* 1.3 70.7 - - - +
329G THR* 1.3 61.9 + - - +
339G SER* 3.3 4.0 - - - -
340G ALA* 2.9 39.2 + - + +
342G VAL* 3.5 25.8 - - + -
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Residues in contact with THR 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284G THR 3.7 0.7 - - - +
285G TRP* 3.3 9.7 - - - -
286G GLU* 2.8 58.4 + - + +
287G LEU 4.4 6.1 - - - +
289G ASN* 5.9 1.6 - - - +
327G TYR 5.2 0.4 - - - +
328G TYR* 1.3 74.2 - - - +
330G CYS* 1.3 66.4 + - - +
331G SER* 4.3 1.5 + - - +
337G SER* 4.1 12.7 - - - -
338G GLN 3.3 8.1 + - - -
339G SER* 2.8 25.6 + - - -
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Residues in contact with CYS 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247G ILE* 4.5 2.7 - - + -
249G LEU* 3.4 12.5 - - + +
272G CYS* 2.0 49.8 - - - -
283G LEU* 3.9 11.0 - - - -
284G THR 3.3 12.6 - - - -
285G TRP* 3.7 20.8 - - + -
313G LEU* 5.0 0.7 - - - -
329G THR* 1.3 75.2 + - - +
331G SER* 1.3 61.3 + - - +
337G SER* 3.2 1.4 - - - -
338G GLN 2.9 36.4 + - - +
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Residues in contact with SER 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G LEU* 4.2 3.1 - - - -
283G LEU* 3.5 1.6 - - - -
284G THR* 2.9 38.5 + - - -
329G THR* 4.2 2.6 - - - -
330G CYS* 1.3 74.3 - - - +
332G SER* 1.4 60.4 + - - +
335G HIS 5.4 0.4 - - - -
337G SER* 3.6 24.9 - - - +
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Residues in contact with SER 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249G LEU* 3.7 14.0 - - - +
281G PHE* 4.6 1.1 - - - -
282G GLY 3.2 13.0 - - - -
283G LEU* 3.9 9.9 - - - -
331G SER* 1.4 75.6 - - - +
333G SER* 1.4 53.9 + - - +
334G LYS 2.8 14.1 + - - -
335G HIS* 2.9 58.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il